README.md
In ramiromagno/ensemblr: R Client for the Ensembl REST API

ensemblr

The goal of {ensemblr} is to provide an R client to the Ensembl REST API.

Please note that this package is still in its infancy and hence only a small fraction of the resources exposed by the Ensembl REST API are retrievable via {ensemblr}. You can check the functionality covered so far in Ensembl REST API Coverage.

You can install the current, very experimental version of {ensemblr} with:

# install.packages("remotes")
remotes::install_github("ramiromagno/ensemblr")

TODO

Retrieve human linkage disequilibrium information for variants within a 1 kilobase window centred on variant 'rs123':

library(ensemblr)
get_ld_variants_by_window('rs123', genomic_window_size = 1L)
#> # A tibble: 6 × 6
#>   species_name population              variant_id1 variant_id2 r_squared d_prime
#>   <chr>        <chr>                   <chr>       <chr>           <dbl>   <dbl>
#> 1 homo_sapiens 1000GENOMES:phase_3:CEU rs123       rs114           0.475   0.703
#> 2 homo_sapiens 1000GENOMES:phase_3:CEU rs123       rs10239961      0.255   1.00 
#> 3 homo_sapiens 1000GENOMES:phase_3:CEU rs123       rs122           0.722   1.00 
#> 4 homo_sapiens 1000GENOMES:phase_3:CEU rs123       rs115           0.721   1.00 
#> 5 homo_sapiens 1000GENOMES:phase_3:CEU rs123       rs124           0.722   1.00 
#> 6 homo_sapiens 1000GENOMES:phase_3:CEU rs123       rs12536724      0.255   1.00

Please note that the {ensemblr} project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

The {ensemblr} logo, ensemblr.png, is a derivative work of an illustration of “The small DNA double helix in PDB entry 309d” by David S. Goodsell and the RCSB PDB, used under CC-BY-4.0. ensemblr.png is licensed under CC-BY-4.0 by Ramiro Magno.